File Formats¶
ORFanage is designed to use simple and common file formats.
Re-Annotated GTF Output¶
SeqID |
chr3 |
Chromosome ID |
|---|---|---|
Source |
BestRefSeq |
Source of the annotation |
Type |
transcript |
Type of the record. Possible values are: transcript/exon/CDS |
Start |
139577792 |
Start coordinate of the record |
End |
139583319 |
End coordinate of the record |
Score |
. |
Unused by ORFanage |
Strand |
Strand of the record |
|
Phase |
. |
Value sets the number of bases that need to be trimmed off the start of the CDS record to reach th estart of the next codon. Value is only available in CDS records. Possible values are: 0/1/2 |
Attributes |
transcript_id “rna-NR_121609.1 |
Field containing extended descriptors of each record |
transcript_id |
rna-NM_001363968.1 |
Unique Transcript Identifier |
|---|---|---|
gene_id |
gene-NMNAT3 |
Unique Gene Identifier |
orfanage_status |
1 |
Flag set if ORFanage was able to find an ORF. Possible values are 0 and 1 |
orfanage_template |
ENST00000643695.2 |
transcript_id of the reference transcript used to find the best ORF |
Extended Stats Output (TSV)¶
query_id |
rna-NR_121609.1 |
rna-NM_001363968.1 |
rna-NM_001363968.1 |
rna-NM_001363968.1 |
rna-XM_011512790.1 |
|---|---|---|---|---|---|
template_id |
ENST00000643695.2 |
ENST00000643695.2 |
ENST00000643695.2 |
ENST00000643695.2 |
|
segment |
139561010-139561392:4294967295 |
139573598-139579055:4294967295 |
139627616-139627724:4294967295 |
139561010-139579055:4294967295 |
|
notes |
gtf |
dup |
gtf |
||
query_len |
393 |
513 |
513 |
648 |
|
template_len |
1041 |
1041 |
1041 |
1041 |
|
pass |
1 |
1 |
0 |
1 |
|
len_match |
383 |
386 |
386 |
648 |
|
len_inframe |
383 |
376 |
376 |
648 |
|
len_outframe |
0 |
10 |
10 |
0 |
|
len_extra |
10 |
127 |
127 |
0 |
|
len_missing |
658 |
655 |
655 |
393 |
|
length_pd |
37.7522 |
49.2795 |
49.2795 |
62.2478 |
|
match_length_pd |
36.7915 |
37.0797 |
37.0797 |
62.2478 |
|
inframe_length_pd |
36.7915 |
36.1191 |
36.1191 |
62.2478 |
|
alignment_match |
0 |
0 |
0 |
0 |
|
pi |
0 |
0 |
0 |
0 |
|
ppp_score |
0 |
0 |
0 |
0 |
